On 10/6/12 8:59 AM, Shima Arasteh wrote:
To use tip3p water model, I copied popc.top and popc.itp in my working
directory. I removed the line of #include tips3p from top file. Also removed
SOL in moleculetypes.
Then I ran genbox :
#genbox -cp popc.gro -cs spc216.gro -o popc-solv.gro -p popc.top
genbox added SOL but there is not any water model including in my top file, so I added
#include "charmm36.ff/tip3p.itp" to top file manually:
Next, I ran energy minimization. Is my procedure correct? How would I be sure that "
tip3p " is used as water model?
Your approach is correct. genbox will not write topology information (i.e.
#include statements) to your topology for you. It adds coordinates to your
configuration and updates the [molecules] section, nothing more. It is up to
you to tell grompp what parameters to apply to the water molecules.
If your topology #includes a TIP3P topology, that's what grompp will use.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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